#MD01_2412.Harada.2006

Row

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Row

temperature (degC)

Uk37 (unitless)

Row

depth_top (cm)

depth_bottom (cm)

age_type (unitless)

age (yr BP)

labcode ()

mat_dated ()

c14_date (RC yr BP)

c14_1s_err (RC yr BP)

delta_r ()

delta_r_original ()

delta_r_1s_error ()

delta_r_1s_error_original ()

other_date ()

other_1s_err ()

other_type ()

---
title: "MD01_2412.Harada.2006"
output: 
  flexdashboard::flex_dashboard:
    vertical_layout: scroll
    theme: bootstrap
    source_code: embed
    orientation: rows
---

```{r setup, include = FALSE}
library(flexdashboard)
library(maptools)
library(tidyverse)
library(purrr)
library(leaflet)
library(plotly)
library(lipdR)
library(dygraphs)
library(geoChronR)
library(lipdverseR)
#read functions
load("../../temp.Rdata")
load("../../chronTemp.Rdata")


#remove columns we don't want to plot
varNames <- sapply(TS, "[[","paleoData_variableName")

# good <- which(!(varNames %in% c("year","depth","age")))
# TS <- TS[good]



#All datasets
dsn <- lipdR::pullTsVariable(TS,"dataSetName")
ui <- which(!duplicated(dsn))
udsn <- dsn[ui]
lat <- lipdR::pullTsVariable(TS,"geo_latitude")[ui]
lon <- lipdR::pullTsVariable(TS,"geo_longitude")[ui]
elev <- lipdR::pullTsVariable(TS,"geo_elevation")[ui]


archiveType <- lipdR::pullTsVariable(TS,"archiveType")[ui]
link <- paste0(udsn,".html") %>%
  str_replace_all("'","_")


#Organize metadata for map
map.meta <- data.frame(dataSetName = udsn, #datasetname
                       lat = lat,#lat
                       lon = lon,#lon
                      # elev = elev,#elevation
                       archiveType = factor(archiveType),#archiveType
                       link = link)#Link


#set index number

i = 385
thisTS <- TS[which(udsn[i] == dsn)]
```
#MD01_2412.Harada.2006

Metadata {.sidebar}
-------------------------------------
[Download LiPD file](MD01_2412.Harada.2006.lpd)
            

[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/MD01_2412.Harada.2006.lpd)
            

[Download paleoData only (csv)](MD01_2412.Harada.2006.csv)
            

[Download chronData only (csv)](MD01_2412.Harada.2006-chron.csv)
            

[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)

root

archiveType: MarineSediment

originalDataUrl: www.ncdc.noaa.gov/paleo/study/9096

lipdVersion: 1.3

pub
pub1

author: list(list(name = "Harada, Naomi; Ahagon, Naokazu; Sakamoto, Tatsuhiko; Uchida, Masao; Ikehara, Minoru; Shibata, Yasuyuki"))

citeKey: KUFYKK47

journal: Global and Planetary Change

volume: 53

pages: 29 46

title: Rapid fluctuation of alkenone temperature in the southwestern Okhotsk Sea during the past 120 ky

pub2
geo

latitude: 44.5275

longitude: 145.004

elevation: -1225

siteName: MD01_2412

PaleoData columns
depth (cm)

TSid: T2L_MD01_2412_depth

variableName: depth

units: cm

description: Sample depth

ageDuplicate (cal years BP)

TSid: T2L_MD01_2412_age_median

variableName: ageDuplicate

units: cal years BP

description: Median age

ageOriginal (BP)

TSid: T2L_MD01_2412_age_original

variableName: ageOriginal

units: BP

description: Original age

ageMedianBacon (cal years BP)

TSid: T2L_MD01_2412_age_medianMedianBacon

variableName: ageMedianBacon

units: cal years BP

description: Median age

age (BP)

TSid: T2L_MD01_2412_age

variableName: age

units: BP

description: Original age

temperature (degC)

TSid: T2L_MD01_2412_uk37_SST_from_uk37

variableName: temperature

units: degC

description: SST calculated from uk37

interpretation
1

direction: positive

variable: T

scope: climate

variableGroup: Temperature

variableGroupOriginal: T

seasonality: annual

seasonalityGeneral: annual

seasonalityOriginal: 1 2 3 4 5 6 7 8 9 10 11 12

variableDetail: sea@surface

variableGroupDirection: list("negative")

Uk37 (unitless)

TSid: T2L_MD01_2412_uk37

variableName: Uk37

units: unitless

ChronData columns
depth_top (cm)

TSid: T2L_MD01_2412_depth_top

variableName: depth_top

units: cm

description: Sample top depth

depth_bottom (cm)

TSid: T2L_MD01_2412_depth_bottom

variableName: depth_bottom

units: cm

description: Sample bottom depth

age_type (unitless)

TSid: RC3BPGwHVg7

variableName: age_type

units: unitless

age (yr BP)

TSid: RbW0YiuMOmH

variableName: age

units: yr BP

labcode ()

TSid: T2L_MD01_2412_labcode

variableName: labcode

description: Lab sample code

mat_dated ()

TSid: T2L_MD01_2412_mat_dated

variableName: mat_dated

description: Material dated

c14_date (RC yr BP)

TSid: T2L_MD01_2412_c14_date

variableName: c14_date

units: RC yr BP

description: 14C date

c14_1s_err (RC yr BP)

TSid: T2L_MD01_2412_c14_1s_err

variableName: c14_1s_err

units: RC yr BP

description: 14C 1-sigma error

delta_r ()

TSid: T2L_MD01_2412_delta_r

variableName: delta_r

description: delta R

delta_r_original ()

TSid: T2L_MD01_2412_delta_r_original

variableName: delta_r_original

description: Original delta R

delta_r_1s_error ()

TSid: T2L_MD01_2412_delta_r_1s_error

variableName: delta_r_1s_error

description: delta R 1-sigma error

delta_r_1s_error_original ()

TSid: T2L_MD01_2412_delta_r_1s_error_original

variableName: delta_r_1s_error_original

description: Original delta R 1-sigma error

other_date ()

TSid: T2L_MD01_2412_other_date

variableName: other_date

description: Other date

other_1s_err ()

TSid: T2L_MD01_2412_other_1s_err

variableName: other_1s_err

description: Other date 1-sigma error

other_type ()

TSid: T2L_MD01_2412_other_type

variableName: other_type

description: Other date type

Row {.tabset .tabset-fade} ----------------------------------------------------------------------- ### Sitemap ```{r} map.meta.split <- split(map.meta, map.meta$archiveType) factpal <- colorFactor("Paired",map.meta$archiveType) buff <- 15 l <- leaflet() %>% addTiles() %>% fitBounds(map.meta$lon[i]-buff,map.meta$lat[i]-buff,map.meta$lon[i]+buff,map.meta$lat[i]+buff) names(map.meta.split) %>% purrr::walk( function(df) { l <<- l %>% addMarkers(data=map.meta.split[[df]], lng=~lon, lat=~lat, label=~as.character(archiveType), popup=~paste(str_c('Dataset: ',dataSetName,''), # str_c("Elevation: ",elev), str_c("Archive Type: ",archiveType), sep = "
"), group = df, clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F), labelOptions = labelOptions(noHide = F, direction = 'auto')) }) l <- l %>% addCircleMarkers(lng = map.meta$lon[i], lat = map.meta$lat[i],radius = 20,color = "red",fillColor = "none") l %>% addLayersControl(position = "bottomleft", overlayGroups = names(map.meta.split), options = layersControlOptions(collapsed = FALSE, opacity = 0.8) ) ``` ### Search the LiPDverse (Beta! doesn't work well yet) ```{r} #Add google search bar htmltools::includeHTML("../../googleSearchChunk.html") ``` Row {.tabset .tabset-fade} ----------------------------------------------------------------------- ### temperature (degC) ```{r} plotCol(thisTS,ind = 5) ``` ### Uk37 (unitless) ```{r} plotCol(thisTS,ind = 4) ``` Row {.tabset .tabset-fade} ----------------------------------------------------------------------- ### depth_top (cm) ```{r} plotCol(chronTS,ind = 2) ``` ### depth_bottom (cm) ```{r} plotCol(chronTS,ind = 3) ``` ### age_type (unitless) ```{r} plotCol(chronTS,ind = 14) ``` ### age (yr BP) ```{r} plotCol(chronTS,ind = 15) ``` ### labcode () ```{r} plotCol(chronTS,ind = 1) ``` ### mat_dated () ```{r} plotCol(chronTS,ind = 4) ``` ### c14_date (RC yr BP) ```{r} plotCol(chronTS,ind = 5) ``` ### c14_1s_err (RC yr BP) ```{r} plotCol(chronTS,ind = 6) ``` ### delta_r () ```{r} plotCol(chronTS,ind = 7) ``` ### delta_r_original () ```{r} plotCol(chronTS,ind = 8) ``` ### delta_r_1s_error () ```{r} plotCol(chronTS,ind = 9) ``` ### delta_r_1s_error_original () ```{r} plotCol(chronTS,ind = 10) ``` ### other_date () ```{r} plotCol(chronTS,ind = 11) ``` ### other_1s_err () ```{r} plotCol(chronTS,ind = 12) ``` ### other_type () ```{r} plotCol(chronTS,ind = 13) ```